Note some or all of this may be due to github desktop's newer version not anymore having a feature to open a project in github.
I, on a Mac, after installing github desktop and atom today, don't have that option
Instead, in github desktop, find out where the local repository is. On a Mac, you can for example open the repository in Finder. Then, in atom you can go to File >> Open, or the equivalent on windows, and in the resulting Finder (or Windows Explorer/Navgiator) popup, go to the repository directory/folder, and open that up. e.g.,